#!/bin/sh

set -e

Tumor=$1
Normal=$2
config_path=$3

source ${config_path}/config.sh

echo ${Tumor}_${Normal}

${gatk4} --java-options "-Xmx10g" Funcotator \
--variant ${vcf_path}/${Tumor}_${Normal}_QC.vcf \
--reference ${seq_ref}/Homo_sapiens_assembly38.fasta \
--ref-version hg19 \
--data-sources-path ${funcotator_ref} \
--output ${maf_path}/${Tumor}_${Normal}_QC.maf \
--output-file-format MAF \
--annotation-default normal_barcode:${Normal} \
--annotation-default tumor_barcode:${Tumor} \
--transcript-selection-mode CANONICAL \
--remove-filtered-variants \
2> ${log_path}/${Tumor}_${Normal}_Funcotator.log
